Showing posts with label disease. Show all posts
Showing posts with label disease. Show all posts

Wednesday, April 20, 2016

Lucky For Me, I’m Diseased

Biology Concepts – disease, vaccination, single nucleotide polymorphisms

Jill Bolte Taylor is an Indiana University neuroscience
professor who suffered a massive stroke. She recognized
what was happening and has translated her thoughts
and feelings into a narrative to help us understand. She
is eloquent in describing how her stroke has affected her
in a positive way. --- Soon to be a major motion picture!

You rarely hear someone say how glad they are to be sick – unless a business meeting, unit test, or visit to the in-laws is involved. Robust health is a sign of good genes, and animals (including humans) instinctually seek out good genes when selecting mates. We don’t like to be sick, and we don’t want others (potential mates) to see us being sick.

True, there is that one person in a thousand who argues quite eloquently that an illness showed them another side of life, expanding their world-view and making them a better person. I applaud this attitude, but did you ever notice that it’s only the survivors that can gain this insight?

Our entire health care system is based on the idea that it is preferable to not be sick. The best way to bring this about is to reduce the chances that we will encounter anything that might provoke a response from our body, including pathogens (disease causing organisms, from pathos = disease and genique = to produce) and allergens (living or non-living molecules that can induce an allergic response).

But what does it mean to be “sick?” If you are infected by a pathogen, are you necessarily sick? There are infections that are subclinical or asymptomatic (without signs of disease), and there are carrier states, when a person is infected and can transmit the disease, but does not have symptoms. Are these people still sick?

You can be in a social situation where you feel empathy or regret, “I feel just sick about how I treated her.” Is this true sickness? Your mental state of mind is important in your health; if you talk yourself into being sick, are you really sick?

Single nucleotide polymorphisms (SNPs) are one base
changes in a gene sequence. “Polymorphism” means
that the population will show different sequences at this
point. SNPs may produce no change in the protein, but in
some cases they may change the shape or function of the
protein just slightly. This may not cause disease, but may
affect the course of a disease, or how drugs will work in
that individual. SNPs may one day lead to personalized
medicines in a new science called pharmacogenomics.
Drugs will be designed to work best for your particular
DNA sequence.

What about genetic mutations? Can everyone with a genetic mutation be considered sick? If yes, then we are all sick, because everyone one of us has thousands, perhaps millions of single nucleotide polymorphisms (differences in a single base of DNA that might lead to change in function of a protein). I would suspect that most of us have larger mutations as well; the older we are, the more mutations we have. Some mutations render a person predisposed (more likely) to develop a disease – is this person sick even before he/she acquires the illness?

Osteoarthritis is a disease that can wear away joint surfaces and necessitate hip or knee replacement. My father has two artificial hips due to osteoarthritis, but does that make him sick or ill?

You see someone coughing, sneezing and blowing his/her nose. It could be due to respiratory allergies or a bacterial or viral infection. Are they sick in one instance, but not the other? I have seen TV ads that try to convince allergy sufferers that they are a menace to society, and should be embarrassed about their condition (unless they use their wonderful product). The entirety of the message in our society is that any illness or condition is a deficit.

To summarize our man-made rule: diseases are bad, and being exposed to diseases is bad, so keep your environment clean and antiseptic. Don’t get me wrong – I am not mocking the rule. I would rather not be sick - so much so that I am careful where I go and what I touch – in some places I simply choose not to breathe, just to be on the safe side. Disease prevention is an important part of life expectancy.

But are there exceptions? Is it sometimes good to get sick, either in general or with some specific disease? I think you know there must be exceptions, otherwise we would just be left with an interesting discussion of what it means to be sick. I bet you can even come up with at least example on your own. There are in fact boatloads of general and specific exceptions to this rule. Let’s take a few weeks and cover a few examples that are exceptions to "disease is bad" rule.

Our first exception is one that you may have already thought of – vaccines. With many vaccines, getting the disease is the key to not getting the disease – counterintuitive, isn’t it? I will use smallpox as an example of the idea that sickness prevents sickness, but there are many others.

Smallpox survivors had a very distinct look. It was
unfortunate that the lesions showed up most heavily on
the face and arms. Thankfully, the disease has been
eradicated, and the virus only exists now in two
laboratories, at the Centers for Disease Control in Atlanta
and the “vector” lab in Siberia. Whether these stocks
should be destroyed is a matter of some debate.
Smallpox, until recently, had been a scourge on mankind for thousands of years. The infection is caused by a virus (Variola major or minor) and may present in several different forms. It was a very dangerous disease, the hemorrhagic form was almost universally lethal. Those that survived smallpox were marked for life (see picture).

In the 1790’s, Edward Jenner of Gloucestershire, England noticed that milk hands and milkmaids seemed to be immune (from Latin, immunis = exempt) to smallpox and he wondered why that might be. The milking workers told him they felt protected because they worked with diseased cows, those that had a mild disease called cowpox. For some reason, having had cowpox kept the milkmaids from catching smallpox.

It turns out that cowpox and smallpox are enough alike that having one will prevent you from having the other. It was on this basis that Jenner developed the first vaccine (Latin from vaccinus = from cows, coined by Louis Pasteur as a tribute to Jenner). By pricking the skin of a young boy with a needle contaminated with the pus from a young milkmaid with cowpox, Jenner showed that this could prevent infection with smallpox (Jenner wasn’t the first to vaccinate with cowpox, just the first to prove it prevented smallpox).

Contracting cowpox, a mild disease that did not kill or scar, could prevent one from catching smallpox, a terrible disease that often killed and left survivors with permanent reminders of their ordeal. Maybe getting sick ain’t always so bad. We will talk more next week about just how vaccination works to produce a protective immune response.

Cowpox vaccination is an example of using one disease to prevent another, but even 100 years before Jenner it was recognized that you could prevent smallpox by giving people smallpox. Strange, isn’t it? Variolation was performed by blowing ground smallpox scabs up the nose of another person, or by pricking them to place the material under the skin.

The virus in the olds scabs was definitely variola, it was just weakened (attenuated) by its age and its time outside of healthy cells. The virus was recognized by the body and an immune response is mounted, but the virus was too weak to produce a fulminant infection was eliminated by the body. But not before it helped the vicitim become immune to subsequent smallpox infection.

Poliomyelitis infection led to a paralysis of the muscles.
This could include the respiratory muscles, so iron lungs
were used to force air in and out of the patients’ lungs.
Before a vaccine was developed, a treatment was
developed by an unaccredited nurse from Australia.
Sister Elizabeth Kenny overcame much professional and
gender prejudice to show that heat and passive exercise
to retrain muscles was better than the then used
immobilization therapy. Try to see the biopic “Sister
Kenny” on TCM some time.

Attenuated vaccines do carry some risk. Paralytic poliomyelitis has almost been eradicated thanks to Jonas Salk’s inactivated (dead) vaccine injections and Sabin’s orallly taken, attenuated vaccine. The attenuated vaccine is better at preventing a natural infection, but in rare cases the vaccine virus can revert back to a wild form and result in iatrogenic (iatro = doctor and genique = to cause) polio, also called vaccine associated paralytic poliomyelitis (VAPP). Thankfully, widespread use of the Salk and Sabin vaccines in the 1950’s has made vaccination in the US (as of 2000) and UK (2004) unnecessary.

Many of the vaccines used today are engineered in a laboratory from just a portion of the organism. By using only the antigenic portion (that part that elicits an immune response) of the virus, there is no risk of iatrogenic disease. If the viral portion is produced in a laboratory using DNA technologies, it is called a recombinant vaccine. In some cases, the antigenic part of the virus is weak on its own, so these subunit vaccines may be conjugated (joined to) some other molecule that will elicit a stronger immune response.

Unfortunately, there is a growing number of people ignoring history and putting are their children and the population at large at risk. Some parents’ reluctance to vaccinate is based on a single 1998 study in which vaccination was linked to autism, even though the author of the paper, Andrew Wakefield, has been convicted of scientific fraud and banned from the practice of medicine. Wakefield was an investor in a company that was going to offer medical testing for vaccine-associated autism and as well as assist in autism/vaccine lawsuits, so he falsified his data in an effort to make his company profitable.  

As a result of the vaccine scare, the UK has seen a rise in the number of measles, mumps, and rubella cases in the last decade. These are diseases associated with childhood, but can cause severe disease or death in many victims, especially adults.

Pertussis, also called whooping cough, is transmitted only
from person to person. If no around you has it, you can’t
get it. However, symptoms may not show for 6 weeks after
infection, so everyone should be vaccinated. The coughing
can be so violent that it breaks blood vessels around the
eyes and nose – and it can kill young children.

Many in the US are also selecting to apply for vaccination exemption due to medical, religious, or personal beliefs; therefore, disease incidence is rising in America as well. In July, 2012, the CDC reported that the US had 18,000 cases of pertussis (whooping cough) in the past year, including an epidemic of more than 2500 cases in Washington state from January to June. This points out the need for vigilance in monitoring, as some of these patients had been vaccinated. This suggests that that the protection may not be lifelong; a booster vaccination may be necessary, although it is also telling that Washington state has one of the highest vaccination exemption rates in the country.

This also brings up the idea of herd immunity. There are some people who have been vaccinated, but protection is not complete. The elderly may not be able to react completely even if vaccinated, as might the very young. Some vaccinations may not take - how many time have you had an antibody titer test to make sure your vaccine worked? It is very rare to get titers unless something is suspected and you are already sick. Therefore, many people must count on the vaccination of the herd - a critical percentage of population needs to be protected in order to keep the incidence of the disease below a crucial level. If the level rises - as with too many people choosing not to vaccinate - then the incidence will sky rocket because it will affect those people who don't happen to know they are not protected. Un vaccinated people affect everyone, not just themselves.

Next week we will look at vaccine driven immune responses in a bit more depth, in an effort to understand why we have to get a flu vaccination every year.

Centers for Disease Control and Prevention (CDC) (2012). Pertussis epidemic - washington, 2012. MMWR. Morbidity and mortality weekly report, 61, 517-22 PMID: 22810264

For more information on these subjects, or classroom activities, see:

Sick/diseased/ill:

Single nucleotide polymorphisms and pharmacogenomics:

Vaccines:

Lack of vaccination:

Wednesday, September 17, 2014

Should I Stay Or Should I Go

Biology concepts – bacteria, motility, flagella, quorum sensing, bacterial swarming, biofilms, pathogenesis


Nomads are wanderers. They come in different flavors.
Hunter-gatherers follow the animals as they graze in
different places. Pastoral nomads have animal herds and
move them around to where the grazing is best. But the
interesting ones are the peripatetic nomads. These are
people that move around within cities and other
populated areas, often to sell services or trades. Romanis,
or gypsies as they are sometimes called, are a
group of peripatetic nomads.
We humans have complex interactive behaviors with one another - these can make things better or, oh so much worse. We form herds as nomadic tribes, or we settle to form cities. Each has its own set of niches and behaviors that must be fulfilled by members of the group. But, it's important that we realize that we aren’t doing anything new, apparently bacteria have been roaming and settling for billions of years.

Our current series has been talking about flagella and how they help bacteria become motile (amongst other things). A relatively new discovery has opened our eyes to an exceptional movement by flagellated bacteria, swarming.

Swimming is when a bacterium on a liquid/surface interface or in liquid moves around by itself using its flagella as a propeller. But groups of bacteria can use their flagella to create a swarm; a mass of bacteria moving as one unit, often faster than the individuals can move on their own.

Bacteria moving as a unit is like tribes of humans moving from one place to another. But there are also those bacteria that choose to hunker down in one location and build a “city.” This prokaryotic Gotham is called a biofilm. We should do a whole series on biofilms, but for now let’s just talk about them in general.

When a number of bacteria of the same type, or sometimes even of different types, are in the same place at the same time, they may begin to form a biofilm. Certain bacteria will secrete proteins as filaments, polysaccharides in the form of slime, and some other structures. All of these together form a network of tunnels, tubules, cavities, and surfaces onto which the bacteria adhere. The biofilm also adheres to whatever surface is nearby. It’s a bacterial city.


The plaque on your teeth is a biofilm. The saliva and
crevicular fluid (between root and gum) provides some
proteins and sugars to build the film. Above is a
photomicrograph of plaque showing that yeast and
bacteria are both involved in mature plaque.
The biofilm matures over time, and different bacteria will have different jobs. The bacteria are stronger together than they are on their own, since the biofilm can prevent antibacterial agents from working. Biofilms are turning out to be important virulence factors (structures that enhance an organism’s ability to cause disease) and are crucial for pathogenesis (patho = disease, and genesis = beginning or course).

Some bacterial colonies settle to form cities and some move on en masse to another location – it really does sound like humans tribes. But biofilms and swarming are not mutually exclusive, in some cases you will see the bacteria at the edge of a biofilm start to swarm and expand, just like urban sprawl creates bigger cities.

There's organization to the swarm as well. Swarming isn’t an, “Everybody run!” kind of movement. Swarming requires controls, regulation, and numerous gene products spread out over the colony. Even though they work as a group, the bacteria might not all go the same direction.

Since bacteria divide by binary fission (one form of asexual reproduction), they tend to form masses in one location, often circular. When they give the signal(s) to swarm, some may take off in this direction, and some in another, based on where they are in the circle. Look at the picture below and right. Pretty, but it shows that colony swarm has multiple leading edges that will travel out into the unknown, and part of the colony will follow behind each.

Every once in a while, a new leading edge might branch off and swarm in a different direction, taking some followers with it. Other types of bacteria seem to swarm equally in all directions, forming concentric circles of new colonies.


This is a false color image showing the branching of a
bacteria colony in a swarm. Dr. Eshel Ben-Jacob from
Tel Aviv University produces these images as science
and art. See many of his images at this site.
The disease-causing bacteria Pseudomonas aeruginosa branches when it swarms, but even this is coordinated. A 2014 paper used a computer to model the branches seen in P. aeruginosa. They occur over a very narrow range of parameters. This means that the bacteria are limiting their activities and conducting themselves within a finely adapted range of behaviors and signals. Bottom line - their movement isn’t random.

Many behaviors occur in swarming bacteria that don’t occur in swimming bacteria. The leading edge cells may secrete surfactant, a combination of chemicals that reduce the surface tension on the plane so that the bacteria can move with less resistance.

The leading edge bacteria grow extra flagella, become elongated, and secrete slime for easy movement - but only the leading edge cells. They band together, becoming like rafts; in fact that’s what they’re called, rafts. The movement of the leading edge plows a furrow in the material they're moving across. This is partly due to the leading edge cells, but it has more to do with the cells behind them. The following cells form roiling masses, and together they push the leading edge along, like pushing a plow to form a ditch for planting seeds.

The furrows are then followed and expanded by the cells behind the leading edge, growing larger and easier to follow. That way, they can push the leading edge better. All these changes and functions lead to faster movement, which is why the swarm can move faster than individuals.

One amazing thing discovered in a 2013 series of experiments was that the leading edge cells secrete DNA. This nucleic acid doesn’t function as genetic material, but is apparently important for keeping the leading edge cells together and moving in the same direction, as well as stimulating movement at all. In experiments where this DNA was chewed by enzymes, the swarming movement stopped completely. Amazing - if they were a marching band in a parade, the DNA would be the banner carried by the drum majors that's emblazoned with their school and nickname. Everybody follows the banner and the drum major.

Integral to the concepts of swarming and biofilm development is the idea of multicellularity in bacteria. They're all clones of one another (except for mutation and any lateral gene transfer), but they work together and may take on different jobs, structures, and morphologies. They are working together to accomplish more than they could on their own. That sounds a lot like a multicellular organism where the different cell specialize into different types in order to perform different functions.


On the left is a cartoon that illustrates how the electron
donor hydrogen sulfide can’t donate electrons unless
something is available to accept them. The oxygen is the
acceptor, and the bacteria provide the cable to connect
them. The filaments of bacteria are shown on the right.
Photocredit to Nils Risgaard-Petersen.
One example comes from a 2012 study. Sea floor bacteria that bridge an area of high oxygen and low hydrogen sulfide to one of low oxygen and high hydrogen sulfide actually form filaments that act as power cables. Electron pass long a length of millions of cells to complete a circuit between the two sets of cells and this provides the energy to make ATP. Bacteria seem to work together in tough environments better than humans do on our best day.

We don’t know all the bacteria that are capable of swarming, but it's probably many more than we have found so far. And we aren't sure just why do they do it. Perhaps it's to leave an area of poor food value behind and strike out for better hunting grounds. Moving faster than they would as individuals might be important when trying to find, and then take advantage of a new food source. Eat up before someone else finds it.

Perhaps swarming is for protection. Like for biofilms, there is evidence that bacteria are less susceptible to antibiotics when swarming. Or it may have something to do with the best way to achieve full biochemical development. There are many studies that suggest that infectious organisms must swarm in order to create disease. Please remember, they aren’t trying to cause disease, but it shows that swarming must be important in their colonial development and a byproduct of this may be disease.


Three colonies of the same bacteria that were not clonal (not
from same exact ancestor - A, B, and C) were grown on the same
plate and they expanded in a swarm-like behavior. Where the
different colonies meet is the Dienes line. On the right is a false
color close up of a Dienes line, showing the battlefield. The
black line is 50 µm long.
They may also swarm to protect a new environment. Bacteria from one colony that grow and begin to swarm can tell their brethren apart. They can even discriminate between bacteria of the same type that have come from separate colony. When the two colonies swarm, they set a boundary between them, called a Dienes Line. A 2013 study showed that in Proteus mirabilis, a bacterium that causes urinary tract infections (UTIs), this boundary is really a battleground.

P. mirabilis has the ability to produce a type VI secretion system that acts as a needle. It punctures an adjacent bacterium and injects toxins. When a swarming colony invades another colony, they all start to produce their type VI secretion needles.

They attack any cell that makes contact with them, in a preemptive sort of fashion. There are many friendly fire incidents, but kin will survive the attack while cells from the other colony will be killed (they aren't immune to the specific toxin). The deeper invader is usually the dominant colony and will kill off the other colony, even though they may be of the same strain. Man - bacteria can be ruthless.

The key to both biofilm development and swarming is quorum sensing (quorum is from Latin qui meaning who, it means the number of members that must be present to transact business). The bacteria sense when their numbers reach a certain tipping point because the levels of certain chemicals reach critical concentrations.

We aren’t sure just why one behavior happens instead of the other, the situations that will induce either biofilm formation or swarming, but the number of bacteria and the state of their environment is key. Therefore, if you can stop the quorum sensing, you can stop swarming or biofilm formation, or both. This would be key to battling some pretty nasty infectious organisms since we said they are often important for pathogenesis.


Proteus mirabilis is a bacteria that swarms in concentric
circles. It causes urinary tract infections in both men and
women. In the lower image you can see the many flagella
of the organism – and this is before it starts to swarm and
leading edge organisms differentiate.
Several recent studies (here and here for example) have shown that certain natural or man made chemicals have the ability to interrupt quorum sensing or swarming/biofilms. Even cranberries seem to do the job.

We have discussed in prior posts about the amazing ability of cranberry to prevent UTIs. A 2013 paper shows that at least part of the cranberry's action on UTI-causing P. mirabilis is through the prevention of swarmer cell differentiation. Work with other bacteria shows that it is quorum sensing that is disrupted by the cranberry compounds, so the swarm in P. mirabilis might be stopped via the bacteria not knowing how many of their brothers are around. Bacteria won't pick a fight unless they know their gang is big enough - it's West Side Story in your bladder.

Next week - some prokaryotes don't move. Just like couch potatoes, they wait for someone to bring them their dinner.



Gloag ES, Turnbull L, Huang A, Vallotton P, Wang H, Nolan LM, Mililli L, Hunt C, Lu J, Osvath SR, Monahan LG, Cavaliere R, Charles IG, Wand MP, Gee ML, Prabhakar R, & Whitchurch CB (2013). Self-organization of bacterial biofilms is facilitated by extracellular DNA. Proceedings of the National Academy of Sciences of the United States of America, 110 (28), 11541-6 PMID: 23798445

Deng P, de Vargas Roditi L, van Ditmarsch D, & Xavier JB (2014). The ecological basis of morphogenesis: branching patterns in swarming colonies of bacteria. New journal of physics, 16, 15006-15006 PMID: 24587694

McCall J, Hidalgo G, Asadishad B, & Tufenkji N (2013). Cranberry impairs selected behaviors essential for virulence in Proteus mirabilis HI4320. Canadian journal of microbiology, 59 (6), 430-6 PMID: 23750959

Alteri CJ, Himpsl SD, Pickens SR, Lindner JR, Zora JS, Miller JE, Arno PD, Straight SW, & Mobley HL (2013). Multicellular bacteria deploy the type VI secretion system to preemptively strike neighboring cells. PLoS pathogens, 9 (9) PMID: 24039579


For more information or classroom activities, see:

Quorum sensing –

Biofilms –

Bacterial swarming -